Difference between revisions of "INF-BIOX120 H13 curriculum"
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SAM (and BAM): [http://samtools.sourceforge.net/SAMv1.pdf "Sequence Alignment/Map Format Specification"] by "The SAM/BAM Format Specification Working Group" | SAM (and BAM): [http://samtools.sourceforge.net/SAMv1.pdf "Sequence Alignment/Map Format Specification"] by "The SAM/BAM Format Specification Working Group" | ||
| − | FASTQ: Peter J. A. Cock | + | FASTQ: Peter J. A. Cock et al<br>Nucleic Acids Res. 2010 April; 38(6): 1767–1771<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/ The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants]<br><br> |
| + | |||
| + | === RNA-Seq === | ||
| + | |||
| + | Anders S et al.<br>Nat Protoc. 2013 Sep;8(9):1765-86<br>[http://www.ncbi.nlm.nih.gov/pubmed/23975260 Count-based differential expression analysis of RNA sequencing data using R and Bioconductor]<br> | ||
| + | |||
| + | <span style="line-height: 1.5em;">Iyer MK & Chinnaiyan AM.</span><br>Nat Biotechnol. 2011 Jul 11;29(7):599-600<br>[http://www.ncbi.nlm.nih.gov/pubmed/21747384 RNA-Seq unleashed]<br> | ||
| + | |||
| + | <span style="line-height: 1.5em;">Trapnell C et al.</span><br>Nat Protoc. 2012 Mar 1;7(3):562-78<br>[http://www.ncbi.nlm.nih.gov/pubmed/22383036 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks]<br> | ||
=== Assembly === | === Assembly === | ||
| Line 31: | Line 39: | ||
Niranjan Nagarajan & Mihai Pop<br>Nature Reviews Genetics 14, 157-167<br>[http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html Sequence assembly demystified]<br> | Niranjan Nagarajan & Mihai Pop<br>Nature Reviews Genetics 14, 157-167<br>[http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html Sequence assembly demystified]<br> | ||
| − | Jason R. Miller, Sergey Koren | + | Jason R. Miller, Sergey Koren and Granger Sutton<br>Genomics Volume 95, Issue 6, June 2010, Pages 315–327<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/ Assembly algorithms for next-generation sequencing data]<br> |
Adam M Phillippy, Michael C Schatz and Mihai Pop<br>Genome Biology 2008, 9:R55<br>[http://genomebiology.com/content/9/3/R55 Genome assembly forensics: finding the elusive mis-assembly]<br> | Adam M Phillippy, Michael C Schatz and Mihai Pop<br>Genome Biology 2008, 9:R55<br>[http://genomebiology.com/content/9/3/R55 Genome assembly forensics: finding the elusive mis-assembly]<br> | ||
Revision as of 10:46, 3 September 2013
Contents
Required curriculum for credit students
The curriculum consists of these four papers:
Metzker, ML
Nat Rev Genet. 2010 Jan;11(1):31-46
Sequencing technologies - the next generation.
Nielsen R, Paul JS, Albrechtsen A, Song YS.
Nat Rev Genet. 2011 Jun;12(6):443-51
Genotype and SNP calling from next-generation sequencing data.
Oshlack A, Robinson MD, Young MD.
Genome Biol. 2010;11(12):220
From RNA-seq reads to differential expression results.
Flicek P, Birney E.
Nat Methods. 2009 Nov;6
Sense from sequence reads : methods for alignment and assembly
Suggested reading
File formats
SAM (and BAM): "Sequence Alignment/Map Format Specification" by "The SAM/BAM Format Specification Working Group"
FASTQ: Peter J. A. Cock et al
Nucleic Acids Res. 2010 April; 38(6): 1767–1771
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
RNA-Seq
Anders S et al.
Nat Protoc. 2013 Sep;8(9):1765-86
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
Iyer MK & Chinnaiyan AM.
Nat Biotechnol. 2011 Jul 11;29(7):599-600
RNA-Seq unleashed
Trapnell C et al.
Nat Protoc. 2012 Mar 1;7(3):562-78
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Assembly
Niranjan Nagarajan & Mihai Pop
Nature Reviews Genetics 14, 157-167
Sequence assembly demystified
Jason R. Miller, Sergey Koren and Granger Sutton
Genomics Volume 95, Issue 6, June 2010, Pages 315–327
Assembly algorithms for next-generation sequencing data
Adam M Phillippy, Michael C Schatz and Mihai Pop
Genome Biology 2008, 9:R55
Genome assembly forensics: finding the elusive mis-assembly
